Tuning Hydrogen Bond Strength in GC (WC), GC* (HG), and GC⁺ (HG) Base Pairs via Substituents: An Interacting Quantum Atoms Analysis

Precise control over DNA stability and interactions is crucial for successful gene editing technologies. To achieve this, a detailed understanding of individual hydrogen bonds within GC (Watson‐Crick) and GC*/GC + (Hoogsteen) base pairs is essential, particularly regarding how strategic substitution of these base pairs modulates their strength and, ultimately, DNA stability. Leveraging the atomic‐resolution capabilities of interacting quantum atoms (IQA) and interacting quantum fragments (IQF) analyses, this study investigates the impact of substituent position and electronic nature on individual hydrogen bond strengths in substituted GC (WC), GC* (HG) and GC + (HG) base pairs. Our results reveal how the electronic properties of substituents and their specific location on the base pairs significantly influence the forces governing atomic interactions, ultimately impacting the strength of individual hydrogen bonds within GC (WC), GC* (HG) and GC + (HG) base pairs. While IQA highlights the importance of classical interactions in stabilizing hydrogen bonds, IQF analysis, taking a more holistic perspective, reveals a more significant role for electron sharing, highlighting the intricate dance between these forces in shaping DNA stability. Furthermore, GC + (HG) base pairs consistently exhibit stronger inter‐fragment interactions compared to GC (WC) and GC* (HG) base pairs, consistent with their higher energy binding energies. The primary reason for the enhanced stability of the GC + (HG) base pairs compared to the GC (WC) and GC* (HG) base pairs is that cytosine has added a proton to the Hoogsteen geometry, leading to strong inter‐fragment interactions. By contrast, GC* (HG) geometries are substantially less favorable than GC (WC) and GC + (HG) geometries. GC* (HG) base pairs consistently show weaker inter‐fragment interactions compared to GC (WC) and GC + (HG) bases. This reduction in stability is attributed to the substitution of the cytosine amino group with its imino tautomeric form at the electron‐donating site of hydrogen bond a , which leads to a decrease in electron‐donating ability and the polarity of the NH bond. Our findings demonstrate the feasibility of tuning the interactions within GC (WC), GC* (HG) and GC + (HG) base pairs through strategic substitution, offering a powerful tool for manipulating DNA stability, function, and interactions with other molecules.